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BCMB 3100- Midterm Exam Guide - Comprehensive Notes for the exam ( 34 pages long!)
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Department
Biochemistry and Molecular Biology
Course Code
BCMB 3100
Professor
Dr.Lemons

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UGA
BCMB 3100
Midterm EXAM
STUDY GUIDE
Unit 4 Lecture: Notes 11/10
Proteins are the essential building blocks for cells, serve as enzymes, etc They’re regulatory.
Proteins are digested to amino acids.
o Trypsin is activated by enterokinase it activates chymotrypsin, carboxypeptidase, and
more trypsin
o Each enzyme breaks down peptide bonds at 1 or more specific locations in a polypeptide
chain
o Dipeptidases released by the duodenum split the small peptides to amino acids
The liver plays a key role in protein metabolism.
o Amino acids can be broken down catabolic or anabolic
o Amino acids are used for protein synthesis
o The liver removes excess amino acids from the circulation, removes the amino group,
and produces ammonia
o Deamination of amino acids and the conversion of the amino groups to urea take place in
the liver.
Ammonia is converted into urea and excreted from the body
o Most proteins are synthesized in the liver.
Excess nitrogen is excreted in 3 forms: ammonia, urea, and uric acid.
Fates of the carbon skeletons of amino acids include:
o Keto acid is composed of 2 components: glucogenic amino acids and ketogenic amino
acids
Glucogenic- an amino acid whose carbon skeleton can be converted into
substrates for gluconeogenesis
Ketogenic- amino acids whose carbon skeletons are degraded into acetyl CoA or
acetoacetyl CoA
Aminotransferase (transaminases)- a class of enzymes that transfer and alpha-amino group from
an alpha-amino acid to an alpha-keto acid.
o Transamination- the amino group is transferred to keto acid acceptor forming the amino
acid products regenerating the enzyme
Urea cycle is critical to production of urea. This cycle converts excess ammonia into urea.
o Part of the cycle takes place in the mitochondria and part in the cytosol.
o Fumarate and aspartate are the direct links to the citric acid cycle.
Furmate is a citric acid cycle intermediate.
Aspartate comes from transamination of oxaloacetate which is also a citric acid
cycle intermediate.
The relationship between amino acid metabolism and the citric acid cycle is that the catabolic
breakdown of amino acids produces intermediates for the citric acid cycle. The anabolic
formation of amino acids uses intermediates from the citric acid cycle as precursors.
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find more resources at oneclass.com
Lecture notes 11/15
Review of Case Study
Question 4
In mammals, glutamate dehydrogenase is allosterically inhibited by GTP and stimulated by ADP.
When AMP is high, the reaction is more rapid.
When ATP is high, the reaction is inhibited.
Question 5
When you lower energy charge aka lower ATP, the reaction will be inhibited.
Glutamate dehydrogenase works best when there is a low energy charge (such as AMP), so
lowering the energy charge improves the catalyzing via glutamate dehydrogenase.
Question 7
The production of carbamoyl phosphate is regulated.
o It’s an irreversible step.
o ATP is utilized (2 ATP)
Question 8
Conversion to: acetyl CoA, acetoacetyl CoA, pyruvate, oxaloacetate, fumarate, succinyl CoA,
and alpha-ketolgutarate.
Question 11
Incorporate ammonium ion (NH4+) into a carbon skeleton.
Glutamate dehydrogenase
o Using glutamate or glutamine and carbon skeletons, you can make all the other amino
acids.
Question 12
Cumulative feedback inhibition- a form of regulation where the enzymes catalyzing the
committed step common to several pathways, is incrementally inhibited by products of each
pathways.
o Each inhibitor can reduce the activity of the enzyme even if the other inhibitors are bound
at saturating level.
o The enzyme has multiple binding sites for different allosteric effectors.
How’s it different from regulate feedback inhibition?
Briefly summarize what’s happening in these pathways: C. glutamicum is an aerobic organism
that’s used for the production of amino acids. The amino acids made C. glutamicum include L-
isoleucine and L-valine. L-valine is synthesized from pyruvate via four reactions. The last
intermediate of L-valine synthesis is Ketoisovalerate which is a precursor for L-leucine and D-
pantothenate
biosynthesis.
Question 14
Interpreting the chart and table: Mutation shows the most inhibition to feedback inhibition? M8
With a mutation, there’s no inhibition, so you’ll see a rise in the amino acid (valine, isoleucine,
and leucine) numbers.
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find more resources at oneclass.com

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[BCMB 3100] Comprehensive fall guide including any lecture notes, textbook notes and exam guides.find more resources at oneclass.com Unit 4 Lecture: Notes 11/10  Proteins are the essential building blocks for cells, serve as enzymes, etc… They’re regulatory.  Proteins are digested to amino acids. o Trypsin is activated by enterokinase  it activates chymotrypsin, carboxypeptidase, and more trypsin o Each enzyme breaks down peptide bonds at 1 or more specific locations in a polypeptide chain o Dipeptidases released by the duodenum split the small peptides to amino acids  The liver plays a key role in protein metabolism. o Amino acids can be broken down catabolic or anabolic o Amino acids are used for protein synthesis o The liver removes excess amino acids from the circulation, removes the amino group, and produces ammonia o Deamination of amino acids and the conversion of the amino groups to urea take place in the liver.  Ammonia is converted into urea and excreted from the body o Most proteins are synthesized in the liver.  Excess nitrogen is excreted in 3 forms: ammonia, urea, and uric acid.  Fates of the carbon skeletons of amino acids include: o Keto acid is composed of 2 components: glucogenic amino acids and ketogenic amino acids  Glucogenic- an amino acid whose carbon skeleton can be converted into substrates for gluconeogenesis  Ketogenic- amino acids whose carbon skeletons are degraded into acetyl CoA or acetoacetyl CoA  Aminotransferase (transaminases)- a class of enzymes that transfer and alpha-amino group from an alpha-amino acid to an alpha-keto acid. o Transamination- the amino group is transferred to keto acid acceptor forming the amino acid products regenerating the enzyme  Urea cycle is critical to production of urea. This cycle converts excess ammonia into urea. o Part of the cycle takes place in the mitochondria and part in the cytosol. o Fumarate and aspartate are the direct links to the citric acid cycle.  Furmate is a citric acid cycle intermediate.  Aspartate comes from transamination of oxaloacetate which is also a citric acid cycle intermediate.  The relationship between amino acid metabolism and the citric acid cycle is that the catabolic breakdown of amino acids produces intermediates for the citric acid cycle. The anabolic formation of amino acids uses intermediates from the citric acid cycle as precursors. find more resources at oneclass.com
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